-
Article
A spatiotemporal atlas of mouse liver homeostasis and regeneration
The mechanism by which mammalian liver cell responses are coordinated during tissue homeostasis and perturbation is poorly understood, representing a major obstacle in our understanding of many diseases. This ...
-
Article
Open AccessVGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification
In contrast to rodents, the mechanisms underlying human trophectoderm and early placenta specification are understudied due to ethical barriers and the scarcity of embryos. Recent reports have shown that human...
-
Article
Open Accessc-Jun as a one-way valve at the naive to primed interface
c-Jun is a proto-oncogene functioning as a transcription factor to activate gene expression under many physiological and pathological conditions, particularly in somatic cells. However, its role in early embry...
-
Article
Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination
Human spermatogenesis is a highly ordered process; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here by simultaneously investigating the chromatin a...
-
Article
Open AccessRestricting epigenetic activity promotes the reprogramming of transformed cells to pluripotency in a line-specific manner
Somatic cell reprogramming and oncogenic transformation share surprisingly similar features, yet transformed cells are resistant to reprogramming. Epigenetic barriers must block transformed cells from reprogra...
-
Article
Open AccessSingle cells and transposable element heterogeneity in stem cells and development
Recent innovations in single cell sequencing-based technologies are shining a light on the heterogeneity of cellular populations in unprecedented detail. However, several cellular aspects are currently underut...
-
Article
Open AccessIdentifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE
Transposable elements (TEs) make up a majority of a typical eukaryote’s genome, and contribute to cell heterogeneity in unclear ways. Single-cell sequencing technologies are powerful tools to explore cells, ho...
-
Protocol
Unified Analysis of Multiple ChIP-Seq Datasets
High-throughput sequencing technologies are increasingly used in molecular cell biology to assess genome-wide chromatin dynamics of proteins bound to DNA, through techniques such as chromatin immunoprecipitati...
-
Article
Open AccessJMJD3 acts in tandem with KLF4 to facilitate reprogramming to pluripotency
The interplay between the Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) and transcriptional/epigenetic co-regulators in somatic cell reprogramming is incompletely understood. Here, we demonstrate that the hist...
-
Article
Open AccessPluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2
Oct4, along with Sox2 and Klf4 (SK), can induce pluripotency but structurally similar factors like Oct6 cannot. To decode why Oct4 has this unique ability, we compare Oct4-binding, accessibility patterns and t...
-
Article
Open AccessAn alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis
CTCF plays key roles in gene regulation, chromatin insulation, imprinting, X chromosome inactivation and organizing the higher-order chromatin architecture of mammalian genomes. Previous studies have mainly fo...
-
Article
Open AccessTransposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells
The majority of mammalian genomes are devoted to transposable elements (TEs). Whilst TEs are increasingly recognized for their important biological functions, they are a potential danger to genomic stability a...
-
Article
Publisher Correction: NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming
In the version of this Article originally published, in Fig. 2c, the ‘+’ sign and ‘OSKM’ were superimposed in the label ‘+OSKM’. In Fig. 4e, in the labels, all instances of ‘Ant’ should have been ‘Anti-’. And,...
-
Article
Open AccessPCGF5 is required for neural differentiation of embryonic stem cells
Polycomb repressive complex 1 (PRC1) is an important regulator of gene expression and development. PRC1 contains the E3 ligases RING1A/B, which monoubiquitinate lysine 119 at histone H2A (H2AK119ub1), and has ...
-
Article
NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming
Somatic cell reprogramming by exogenous factors requires cooperation with transcriptional co-activators and co-repressors to effectively remodel the epigenetic environment. How this interplay is regulated rema...
-
Article
Capturing the interactome of newly transcribed RNA
Labeling newly transcribed RNA with 5-ethynyluridine and adding biotin via click chemistry allows the analysis of the proteome bound to the various RNA species, including nascent RNA.
-
Article
Open AccessA sequential EMT-MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes
Reprogramming has been shown to involve EMT–MET; however, its role in cell differentiation is unclear. We report here that in vitro differentiation of hESCs to hepatic lineage undergoes a sequential EMT–MET with ...
-
Article
The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters
Recent studies have boosted our understanding of long noncoding RNAs (lncRNAs) in numerous biological processes, but few have examined their roles in somatic cell reprogramming. Through expression profiling an...
-
Article
Open AccessGenome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling
The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an an...
